Perera, the overnight leader by three shots, came up with a tenacious even-par-70 in the final round to sign off with a winning total of 14-under-266.
Gurgaon-based Digvijay Singh posted the day's best score, a scorching eight-under-62, to finish joint runner-up at 13-under-267 along with Mukesh Kumar (66) of Mhow, the winner of the last edition of the Chennai Open.
Perera (68-63-65-70) had an unexpectedly quiet final day as he managed only two birdies and two bogeys.
There was a four-shot swing against Perera and in favour of Thangaraja over the first five holes that gave the latter a one-shot lead.
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However, Perera played some solid golf that kept him on course even as Thangaraja made a bunch of errors to drop four shots from the 14th to the 16th.
He was back in the lead from the 15th onwards and saw it home despite a bogey on the 17th.
"I was really hungry to win and break my victory drought. This means a lot for me. My family has supported me throughout my lean phase and so have my sponsors," said Perera, who bagged his sixth title on the PGTI.
Digvijay Singh (70-66-69-62) returned a sublime 62, the best score of the day, to climb 11 places from overnight tied 13th to tied second.
Digvijay, a former Asian Tour winner, put together an eagle and seven birdies at the cost of a bogey.
Joining him in tied second was Mukesh Kumar (66-66-69-66), who had won at MGC on the last three occasions.
Mukesh worked his way up from overnight tied fourth after making an eagle, four birdies and two bogeys on Sunday at one of his favourite venues.
Chennai-based rookie Shivnaren Srinivasan fired a final round of 76 to finish tied 45th at seven-over-287.
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